Commander denies charges stemming from ’84 episode

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Governor Deval Patrick placed the head of the Massachusetts National Guard on leave Thursday night after learning that he is under investigation in the alleged rape of a subordinate on a Florida beach 28 years ago while the two were on maneuvers with a military police unit.

The explosive charges against Adjutant General Joseph C. Carter were originally investigated several months after the alleged 1984 assault. The investigating officer recommended that the alleged victim, Susan Pelletier, take the matter to police, but Pelletier told the Globe she was afraid to press charges.

Pelletier’s allegations resurfaced late last year as Carter was under consideration for promotion from one-star to two-star general. It put a freeze on the promotion while military investigators questioned Pelletier and others involved.

“He raped and beat me and left me,’’ said Pelletier, who was a 23-year-old secretary at the time and now lives in Kentucky. Pelletier said she was so traumatized by the assault that she deserted the National Guard for several months to avoid seeing Carter again.

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Carter, a Boston police superintendent at the time of the alleged assault, issued a statement Thursday night flatly denying the attack or even knowing Pelletier.

This is not the first time the rape allegation has come to the attention of top military officials. The officer who conducted the original investigation, Lieutenant Colonel Mark P. Murray, testified about the unresolved allegations against Carter during a failed 2010 court-martial initiated against him by Carter.

Carter, in his statement yesterday, said the rape allegations first came to his attention during Murray’s court-martial, which centered on Carter’s allegations of financial impropriety by Murray.

Murray “claimed a sexual assault allegation was made against me in the early 1980s,’’ Carter said in the statement. “I was shocked by the allegation when it was made in 2010. I categorically denied the allegation in 2010 and continue to deny it today. I don’t know or recall a Susan Pelletier, and I am cooperating in an investigation by the Army.’’

A Patrick aide said yesterday that Carter did not inform the governor about the allegations until Thursday.

“He told the governor that he is innocent of the allegation,’’ said Brendan Ryan, a Patrick spokesman.

Nonetheless, Ryan said that Carter would be placed on administrative leave with pay until the investigation is complete. Carter is paid $173,214 a year by the state, as well as federal compensation, to oversee the nearly 9,000 members of the National Guard, the vast majority of them part-time soldiers.

“The governor will wait for the result of the investigation before taking any action,’’ Ryan said.

Carter, 56, had a distinguished career in law enforcement before Patrick picked him as the first African-American commander of the National Guard in its 370-year history. Carter was the youngest member of the command staff in Boston police history, and he served as chief of the MBTA Transit Police for four years. In between, he was police chief in Oak Bluffs on Martha’s Vineyard.

On weekends, meanwhile, Carter rose through the ranks of the National Guard, which he joined in 1974. By the mid-1980s, he was serving in a military police unit based in Hyannis with Pelletier, who was a secretary.

The alleged rape took place while the unit was on a two-week training mission in Florida after a night of drinking and dancing with a group of Guard members, according to Pelletier. Although the Globe usually does not identify rape victims, it is identifying Pelletier because she chose to speak on the record to describe the alleged assault.

When her supervisors, Captain Charles Mouris and Carter, left to go to the store, she said she asked to go along to buy cigarettes.

As Mouris drove, however, Pelletier said she felt nauseated and asked him to pull over in a beach parking lot.

When she got out of the car, Carter followed, she said.

“We walked on the sand near the water,’’ she said. “He was all over me. My boots were ripped. My clothes were ripped. He raped me. He was violent about it. I remember begging him to leave me alone.’’

She said she was left there, bruised and bloodied, until soldiers from the motor pool discovered her later that night.

Initially, Pelletier decided not to report the attack, she said, in part because she was afraid of Carter. Instead, she asked to transfer to another unit, and, when the request was denied, she stopped reporting for Guard duty. As a result, she said, she received a dishonorable discharge.

But Pelletier said she soon regretted her actions and, several months later, she asked to be reinstated. That is when National Guard officials at headquarters in Milford learned about the rape allegations, and the adjutant general at the time, Anthony C. Spadorcia, asked Murray, then a Guard lawyer, to investigate.

Murray interviewed Pelletier, but not Carter, about the alleged attack before recommending that she take up the matter with civilian police, in part because civilian penalties for rape are more severe than under state military law, which permits only a $200 fine or 200 days in jail.

“This matter was best handled by civilian authorities,’’ Murray said, according to a transcript of the court martial.

Pelletier could not remember Murray’s advice from 1985, but she recalled that she did not file a complaint with the police.

“Why go to the police?’’ she said. “I was military police. What would civilian police do?’’

That might have been the end of the episode if not for a serious falling out between Carter, who rose to become commander of the Guard, and Murray, who was appointed quartermaster, overseeing the guard’s state-owned armories and other property.

In 2010, Carter sought to remove Murray from his job, which, under Massachusetts law, can be accomplished only by seeking a court-martial. Carter accused Murray of offenses including misusing federal money, hiring a convicted felon to do legal work, and threatening a whistleblower.

During his trial, Murray brought up the alleged rape to suggest that Carter was biased against him because he had investigated the charges.

Murray said he reported his findings to Spadorcia, who, in turn, spoke to Carter. According to Murray, Spadorcia quoted Carter as saying, “Well, I hope this doesn’t impact me some time in my future.’’

However, Major John Benson, a prosecutor at the court martial, strongly objected to Murray’s comments, saying that he had no documentation and that Carter had no chance to defend himself.

Murray was cleared of all charges, and he remains the Guard’s quartermaster.

But the rape issue did not go away, in part because the Army is obligated to investigate any allegations of serious misconduct no matter when they occurred. When Carter came up for a promotion, which must be approved by the Army and confirmed by the US Senate, Army investigators began looking into the alleged incident in Florida.

Pelletier said she was shocked when the Army investigator got in touch with her late last year and wanted to discuss her allegations against Carter.

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